Attached is the sietraj.tcl script. Thanks.
On Fri, Apr 11, 2014 at 1:34 PM, Shulin Zhuang <shulin.zhuang.gmail.com>wrote:
> Dear All,
>
> When I run sietraj to calculate the binding free energy of protein-ligand
> complex, I get the error as following. Would you like to help me out?
> My command:
>
> [biomd.bro-login 329] /home/biomd/sietraj/Brimm/bin/sietraj -pt
> com.prmtop -trj 329-nowat.mdcrd -sf 1 -ef 10015 -inc 50 -tr 1-9239 -lr
> 9240-9288 -o 329-sietraj.out -sie
>
> The feedback:
> [biomd.bro-login 329]$ Loaded Britcl-v2.3c-64.so
> Britcl_functions.tcl 353 2013-05-03
> 1 -7.480 8.996 -2921.342 -2928.007 -2.332 -41.720 -1.621 -734.275
> TypeError in method 'Vec3d_y_set', argument 2 of type 'double'
> while executing
> "[$mol GetAtom $i] configure -$axis($actr) [string range $line $istart
> [expr $istart + 7]]"
> (procedure "ReadNextFrameInTrj" line 11)
> invoked from within
> "ReadNextFrameInTrj m1 $fp_trj"
> ("for" body line 3)
> invoked from within
> "for {set iframe $istart} {$iframe <= $iend} {incr iframe $inc} {
> if {$mut2ala == 0} {
> if {[ReadNextFrameInTrj m1 $fp_trj] != 0} {
> pu..."
> (file "/home/biomd/sietraj/Brimm/apps/sietraj/sietraj.tcl" line 142)
>
>
> For the first line:1 -7.480 8.996 -2921.342 -2928.007 -2.332 -41.720
> -1.621 -734.275 these data means sietraj succuessfull calculate the
> binding free energy for the first snapshot. I guess there may be something
> wrong with the tcl of the system.
>
> Much appreciated to your help.
> Shulin
>
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Received on Thu Apr 10 2014 - 23:00:03 PDT
